The prospect of realizing materials with highest strengths and other unique properties has driven a large number of research activities on nanostructured materials in recent years. The present dissertation deals with the atomic-scale modeling of nanocrystalline and nanotwinned metals and alloys, employing state of-the-art atomistic simulation and analysis methods. The aims of the present work are two-fold: to develop novel computational techniques in the field of atomistic materials modeling, and to use these methods to shed light on the structure and atomic-scale plasticity of nanostructured materials. In the first part of this thesis the newly developed data analyis and visualization software Ovito is described, which provides the basis for all following work. It serves as an integral part in the search for the origins of microstrain broadening in x-ray diffraction (XRD) data of nanocrystalline materials. To this end, virtual nanocrystalline structures are characterized by means of simulated diffraction experiments as well as a real-space strain field analysis. By correlating the results from the strain field analysis with the XRD measurements, conclusions on the features of nanometer-sized grains contributing to peak broadening can be drawn. In the second part two sophisticated analysis algorithms are developed, which allow to extract the complete dislocation network from an atomistic simulation. The identification of single dislocation lines and the determination of their Burgers vector has been a laborious task usually done by hand in the past. The new method makes this information available within seconds, enabling a quantitative assessment of dislocation processes in large-scale molecular dynamics (MD) simulations. It is employed in a study of dislocation plasticity of nanotwinned metals, which can exhibt highest strength and ductility compared with their twin-free counterparts. The deformation mechanisms of Cu and Pd with ultrahigh twin densities are investigated by means of MD simulations. While nanotwins have a strengthening effect in Cu, they lead to a softening in Pd. This difference is discussed in terms of the characteristic dislocations occurring during deformation. The third part is dedicated to nanocrystalline alloys. First, an atomistic simulation method is described that allows to model such materials by taking into account both structural and chemical equilibration in large-scale MD simulations. It is complemented by an efficient implementation of a concentration-dependent interatomic potential scheme, which enables a precise description of the energetics of mixing in multi-component systems over the whole concentration range. These tools are then employed in a study of nanocrystalline Pd–Au. The stress-strain behavior of this miscible alloy is discussed in terms of the interplay of grain boundary solute segregation, fault energies, and grain size.